Parallel tempering for dynamic generalized linear models

ABSTRACT

Markov chain Monte Carlo (MCMC) methods can be used for statistical inference. The methods are time-consuming due to time-vary. To resolve these problems, parallel tempering (PT), as a parallel MCMC method, is tried, for dynamic generalized linear models (DGLMs), as well as the several optimal properties of our proposed method. In PT, two or more samples are drawn at the same time, and samples can exchange information with each other. We also present some simulations of the DGLMs in the case and provide two applications of Poisson-type DGLMs in financial research.     

Augmented mixed beta regression models with skew-normal independent distributions: Bayesian analysis of labor force data

Abstract

Augmented mixed beta regression models are suitable choices for modeling continuous response variables on the closed interval [0, 1]. The random eeceeects in these models are typically assumed to be normally distributed, but this assumption is frequently violated in some applied studies. In this paper, an augmented mixed beta regression model with skew-normal independent distribution for random effects are used. Next, we adopt a Bayesian approach for parameter estimation using the MCMC algorithm. The methods are then evaluated using some intensive simulation studies. Finally, the proposed models have applied to analyze a dataset from an Iranian Labor Force Survey.     

Model fitting and inference under latent equilibrium processes

This paper presents a methodology for model fitting and inference in the context of Bayesian models of the type f(Y | X,θ)f(X|θ)f(θ), where Y is the (set of) observed data, θ is a set of model parameters and X is an unobserved (latent) stationary stochastic process induced by the first order transition model f(X ^(t+1)|X ^(t),θ), where X ^(t) denotes the state of the process at time (or generation) t. The crucial feature of the above type of model is that, given θ, the transition model f(X ^(t+1)|X ^(t),θ) is known but the distribution of the stochastic process in equilibrium, that is f(X|θ), is, except in very special cases, intractable, hence unknown. A further point to note is that the data Y has been assumed to be observed when the underlying process is in equilibrium. In other words, the data is not collected dynamically over time. We refer to such specification as a latent equilibrium process (LEP) model. It is motivated by problems in population genetics (though other applications are discussed), where it is of interest to learn about parameters such as mutation and migration rates and population sizes, given a sample of allele frequencies at one or more loci. In such problems it is natural to assume that the distribution of the observed allele frequencies depends on the true (unobserved) population allele frequencies, whereas the distribution of the true allele frequencies is only indirectly specified through a transition model. As a hierarchical specification, it is natural to fit the LEP within a Bayesian framework. Fitting such models is usually done via Markov chain Monte Carlo (MCMC). However, we demonstrate that, in the case of LEP models, implementation of MCMC is far from straightforward. The main contribution of this paper is to provide a methodology to implement MCMC for LEP models. We demonstrate our approach in population genetics problems with both simulated and real data sets. The resultant model fitting is computationally intensive and thus, we also discuss parallel implementation of the procedure in special cases.     

Gamma shared frailty model based on reversed hazard rate

Abstract

Frailty models are used in survival analysis to account for unobserved heterogeneity in individual risks to disease and death. To analyze bivariate data on related survival times (e.g., matched pairs experiments, twin, or family data), shared frailty models were suggested. Shared frailty models are frequently used to model heterogeneity in survival analysis. The most common shared frailty model is a model in which hazard function is a product of random factor(frailty) and baseline hazard function which is common to all individuals. There are certain assumptions about the baseline distribution and distribution of frailty. In this paper, we introduce shared gamma frailty models with reversed hazard rate. We introduce Bayesian estimation procedure using Markov Chain Monte Carlo (MCMC) technique to estimate the parameters involved in the model. We present a simulation study to compare the true values of the parameters with the estimated values. Also, we apply the proposed model to the Australian twin data set.     

On a nonlinear Birnbaum–Saunders model based on a bivariate construction and its characteristics

Abstract

The Birnbaum-Saunders (BS) distribution is an asymmetric probability model that is receiving considerable attention. In this article, we propose a methodology based on a new class of BS models generated from the Student-t distribution. We obtain a recurrence relationship for a BS distribution based on a nonlinear skew–t distribution. Model parameters estimators are obtained by means of the maximum likelihood method, which are evaluated by Monte Carlo simulations. We illustrate the obtained results by analyzing two real data sets. These data analyses allow the adequacy of the proposed model to be shown and discussed by applying model selection tools.     

Relabel mixture models via modal clustering

Effectively solving the label switching problem is critical for both Bayesian and Frequentist mixture model analyses. In this article, a new relabeling method is proposed by extending a recently developed modal clustering algorithm. First, the posterior distribution is estimated by a kernel density from permuted MCMC or bootstrap samples of parameters. Second, a modal EM algorithm is used to find the m! symmetric modes of the KDE. Finally, samples that ascend to the same mode are assigned the same label. Simulations and real data applications demonstrate that the new method provides more accurate estimates than many existing relabeling methods.     

Bayesian analysis of circular distributions based on non-negative trigonometric sums

ABSTRACT

Fernández-Durán [Circular distributions based on nonnegative trigonometric sums. Biometrics. 2004;60:499–503] developed a new family of circular distributions based on non-negative trigonometric sums that is suitable for modelling data sets that present skewness and/or multimodality. In this paper, a Bayesian approach to deriving estimates of the unknown parameters of this family of distributions is presented. Because the parameter space is the surface of a hypersphere and the dimension of the hypersphere is an unknown parameter of the distribution, the Bayesian inference must be based on transdimensional Markov Chain Monte Carlo (MCMC) algorithms to obtain samples from the high-dimensional posterior distribution. The MCMC algorithm explores the parameter space by moving along great circles on the surface of the hypersphere. The methodology is illustrated with real and simulated data sets.     

Bayesian nonparametric survival analysis using mixture of Burr XII distributions

ABSTRACT

Recently, the Bayesian nonparametric approaches in survival studies attract much more attentions. Because of multimodality in survival data, the mixture models are very common. We introduce a Bayesian nonparametric mixture model with Burr distribution (Burr type XII) as the kernel. Since the Burr distribution shares good properties of common distributions on survival analysis, it has more flexibility than other distributions. By applying this model to simulated and real failure time datasets, we show the preference of this model and compare it with Dirichlet process mixture models with different kernels. The Markov chain Monte Carlo (MCMC) simulation methods to calculate the posterior distribution are used.     

Bayesian analysis of generalized elliptical semi-parametric models

In this paper, we study the statistical inference based on the Bayesian approach for regression models with the assumption that independent additive errors follow normal, Student-t, slash, contaminated normal, Laplace or symmetric hyperbolic distribution, where both location and dispersion parameters of the response variable distribution include nonparametric additive components approximated by B-splines. This class of models provides a rich set of symmetric distributions for the model error. Some of these distributions have heavier or lighter tails than the normal as well as different levels of kurtosis. In order to draw samples of the posterior distribution of the interest parameters, we propose an efficient Markov Chain Monte Carlo (MCMC) algorithm, which combines Gibbs sampler and Metropolis–Hastings algorithms. The performance of the proposed MCMC algorithm is assessed through simulation experiments. We apply the proposed methodology to a real data set. The proposed methodology is implemented in the R package BayesGESM using the function gesm().     

Model based labeling for mixture models

Label switching is one of the fundamental problems for Bayesian mixture model analysis. Due to the permutation invariance of the mixture posterior, we can consider that the posterior of a m-component mixture model is a mixture distribution with m! symmetric components and therefore the object of labeling is to recover one of the components. In order to do labeling, we propose to first fit a symmetric m!-component mixture model to the Markov chain Monte Carlo (MCMC) samples and then choose the label for each sample by maximizing the corresponding classification probabilities, which are the probabilities of all possible labels for each sample. Both parametric and semi-parametric ways are proposed to fit the symmetric mixture model for the posterior. Compared to the existing labeling methods, our proposed method aims to approximate the posterior directly and provides the labeling probabilities for all possible labels and thus has a model explanation and theoretical support. In addition, we introduce a situation in which the “ideally” labeled samples are available and thus can be used to compare different labeling methods. We demonstrate the success of our new method in dealing with the label switching problem using two examples.     

Quantifying uncertainty in transdimensional Markov chain Monte Carlo using discrete Markov models

Bayesian analysis often concerns an evaluation of models with different dimensionality as is necessary in, for example, model selection or mixture models. To facilitate this evaluation, transdimensional Markov chain Monte Carlo (MCMC) relies on sampling a discrete indexing variable to estimate the posterior model probabilities. However, little attention has been paid to the precision of these estimates. If only few switches occur between the models in the transdimensional MCMC output, precision may be low and assessment based on the assumption of independent samples misleading. Here, we propose a new method to estimate the precision based on the observed transition matrix of the model-indexing variable. Assuming a first-order Markov model, the method samples from the posterior of the stationary distribution. This allows assessment of the uncertainty in the estimated posterior model probabilities, model ranks, and Bayes factors. Moreover, the method provides an estimate for the effective sample size of the MCMC output. In two model selection examples, we show that the proposed approach provides a good assessment of the uncertainty associated with the estimated posterior model probabilities.

     

A note on Markov chain Monte Carlo sweep strategies

Markov chain Monte Carlo (MCMC) routines have become a fundamental means for generating random variates from distributions otherwise difficult to sample. The Hastings sampler, which includes the Gibbs and Metropolis samplers as special cases, is the most popular MCMC method. A number of implementations are available for running these MCMC routines varying in the order through which the components or blocks of the random vector of interest X are cycled or visited. The two most common implementations are the deterministic sweep strategy, whereby the components or blocks of X are updated successively and in a fixed order, and the random sweep strategy, whereby the coordinates or blocks of X are updated in a randomly determined order. In this article, we present a general representation for MCMC updating schemes showing that the deterministic scan is a special case of the random scan. We also discuss decision criteria for choosing a sweep strategy.     

Diffusive nested sampling

We introduce a general Monte Carlo method based on Nested Sampling (NS), for sampling complex probability distributions and estimating the normalising constant. The method uses one or more particles, which explore a mixture of nested probability distributions, each successive distribution occupying ∼e ⁻¹ times the enclosed prior mass of the previous distribution. While NS technically requires independent generation of particles, Markov Chain Monte Carlo (MCMC) exploration fits naturally into this technique. We illustrate the new method on a test problem and find that it can achieve four times the accuracy of classic MCMC-based Nested Sampling, for the same computational effort; equivalent to a factor of 16 speedup. An additional benefit is that more samples and a more accurate evidence value can be obtained simply by continuing the run for longer, as in standard MCMC.     

A new discrete probability distribution with integer support on (−∞, ∞)

ABSTRACT

A new discrete probability distribution with integer support on (?∞, ∞) is proposed as a discrete analog of the continuous logistic distribution. Some of its important distributional and reliability properties are established. Its relationship with some known distributions is discussed. Parameter estimation by maximum-likelihood method is presented. Simulation is done to investigate properties of maximum-likelihood estimators. Real life application of the proposed distribution as empirical model is considered by conducting a comparative data fitting with Skellam distribution, Kemp's discrete normal, Roy's discrete normal, and discrete Laplace distribution.     

Shared frailty models with baseline generalized Pareto distribution

Abstract

In this article, we have considered three different shared frailty models under the assumption of generalized Pareto Distribution as baseline distribution. Frailty models have been used in the survival analysis to account for the unobserved heterogeneity in an individual risks to disease and death. These three frailty models are with gamma frailty, inverse Gaussian frailty and positive stable frailty. Then we introduce the Bayesian estimation procedure using Markov chain Monte Carlo (MCMC) technique to estimate the parameters. We applied these three models to a kidney infection data and find the best fitted model for kidney infection data. We present a simulation study to compare true value of the parameters with the estimated values. Model comparison is made using Bayesian model selection criterion and a well-fitted model is suggested for the kidney infection data.     

Sampling hyperparameters in hierarchical models: Improving on Gibbs for high-dimensional latent fields and large datasets

ABSTRACT

A common Bayesian hierarchical model is where high-dimensional observed data depend on high-dimensional latent variables that, in turn, depend on relatively few hyperparameters. When the full conditional distribution over latent variables has a known form, general MCMC sampling need only be performed on the low-dimensional marginal posterior distribution over hyperparameters. This improves on popular Gibbs sampling that computes over the full space. Sampling the marginal posterior over hyperparameters exhibits good scaling of compute cost with data size, particularly when that distribution depends on a low-dimensional sufficient statistic.     

On the two-parameter Bell–Touchard discrete distribution

Abstract

In this paper we introduce a new two-parameter discrete distribution which may be useful for modeling count data. Additionally, the probability mass function is very simple and it may have a zero vertex. We show that the new discrete distribution is a particular solution of a multiple Poisson process, and that it is infinitely divisible. Additionally, various structural properties of the new discrete distribution are derived. We also discuss two methods (moments and maximum likelihood) to estimate the model parameters. The usefulness of the proposed distribution is illustrated by means of real data sets to prove its versatility in practical applications.     

Estimation and prediction of the Kumaraswamy distribution based on record values and inter-record times

ABSTRACT

The maximum likelihood and Bayesian approaches for estimating the parameters and the prediction of future record values for the Kumaraswamy distribution has been considered when the lower record values along with the number of observations following the record values (inter-record-times) have been observed. The Bayes estimates are obtained based on a joint bivariate prior for the shape parameters. In this case, Bayes estimates of the parameters have been developed by using Lindley's approximation and the Markov Chain Monte Carlo (MCMC) method due to the lack of explicit forms under the squared error and the linear-exponential loss functions. The MCMC method has been also used to construct the highest posterior density credible intervals. The Bayes and the maximum likelihood estimates are compared by using the estimated risk through Monte Carlo simulations. We further consider the non-Bayesian and Bayesian prediction for future lower record values arising from the Kumaraswamy distribution based on record values with their corresponding inter-record times and only record values. The comparison of the derived predictors are carried out by using Monte Carlo simulations. Real data are analysed for an illustration of the findings.     

A bivariate mixture of negative binomial distributions and its applications

Abstract

We construct a new bivariate mixture of negative binomial distributions which represents over-dispersed data more efficiently. This is an extension of a univariate mixture of beta and negative binomial distributions. Characteristics of this joint distribution are studied including conditional distributions. Some properties of the correlation coefficient are explored. We demonstrate the applicability of our proposed model by fitting to three real data sets with correlated count data. A comparison is made with some previously used models to show the effectiveness of the new model.     

The exponentiated-log-logistic geometric distribution: Dual activation

ABSTRACT

The log-logistic distribution is commonly used to model lifetime data. We propose a wider distribution, named the exponentiated log-logistic geometric distribution, based on a double activation approach. We obtain the quantile function, ordinary moments, and generating function. The method of maximum likelihood is used to estimate the model parameters. We propose a new extended regression model based on the logarithm of the exponentiated log-logistic geometric distribution. This regression model can be very useful in the analysis of real data and could provide better fits than other special regression models. The potentiality of the new models is illustrated by means of two applications to real lifetime data sets.